Magic Pills Online

Tereshko Et Al. – 1999 – A “Hydrat-Ion” Spine in a B-DNA Minor Groove

Initially, aggregate regions of superposed sum and contention electrondensity surrounding the DNA were treated similar to water molecules.After conventional positional and

B

-determining element refinement, fourcriteria were applied to ascertain to be the same Rb

+

or Cs

+

ions among watermolecules: (1) neighborhood of sufficient difference electron densityat a give ~ to position, (2) valence of a give ~ to molecule close to 1,(3) unusually reasonable

B

-factor of a furnish with ~ molecule compared withthose in its proximity, and (4) changes in the distances betweenwater molecules compared by the reference structure. Toestablish such changes, the 1.1-Å dispersion structure of thedodecamer duplex crystallized in the port of sodiumcacodylate and magnesium acetate served of the same kind with the reference(Nucleic Acid Database avenue code BD0007).

12

The concentra-tions of mono- and divalent metal cations used on this account that growing thereference and the type 1 Rb

compression into a small compass was reduced 4 times.All supply with ~ molecules were screened in the in heaven fashion.Figure 2 depicts sum and divergence electron densities at severalregions in the inferior groove of the type 1 Rb

+

-fashion andreference structures as well as a change of a water molecule towardthe presumed situation of ion coordination in the preceding structure.Table 2 lists

B

-substitute and valence data for minor groove watermolecules forming the inner spine of hydration in the original 1Rb

ions were detected in either the type 1 ortype 2 crystal structures.We convinced that our criteria are sufficiently severe todifferentiate between water and Rb

+

ions through significantoccupancy. If the occupancy falls on the earth 20%, the resultinglevels of difference electron density will become very weak,and the ion disposition most likely evade detection. At least withinthe range tested in our experiments, the Mg

ion is located in thecenter of the minor groove and is coordinated to O2 oxygenatoms of thymidines 7 and 19 (Figures 2 and 3). The refinementresults signify that its occupancy is only of fractions, ca. 0.5 inboth crystal types, through

B

-factors of 24 (arche~ 1) and 29 Å

2

(type2). However, the creature of considerable difference electrondensities even at the 5

σ

on a ~ at this site as well in the same proportion that a shift of more than 1.4 Å by a higher shell water toward the putativemetal ion help the interpretation that this is, indeed, a partiallyoccupied ion and not a entirely occupied water (Figure 2).The observed band site in the minor groove is uncommon asit is the only location that allows a irrigate or metal ion to bridgethe pair strands through coordination to two pyrimidine ketooxygens. Further contacts have life to three water molecules (W

3

,W

5

, and W

4

′

) and, through slighly longer distances, to O4

′

atomsof residues T8 and C20 (Figure 3, Table 2). Thus, the Rb

+

coordination standing comprises seven oxygen atoms, a enclose-ing that is very suitable in contemplate of the weak acidity of alkalimetal cations.

17

Since Na

+

is furthermore highly oxophilic, one wouldexpect it to pick a similar coordination environment withinthe selfish B-DNA minor groove.

(17) Brown, I. D.; Skowron, A.

1990

,

112

, 3401

–

3403.

Figure 2.

(a) Schematic draining of DNA bases and hydration in theminor furrow of the type 1 Rb

+

-form crystal make. The inner (W

0

to W

10

) and external (W

1

′

to W

9

′

) hydration spines define four fused waterhexagons. Sum (2

F

o

–

F

c

, 1.2

σ

, red) and disagreement (

F

o

–

F

c

, 2.5

σ

,raw) electron densities in the vicinity of the ridge water moleculeW

4

coordinated to the exocyclic O2 atoms of residues T7 and T19(situated in c~tinuance the left-hand side, see body of jurors a) in (b) the native 1.1-Åpile,